User-Populated Online Repository of Science Protocols

ABSTRACT

Systems, apparatus and methods are provided to maintain a user-populated online repository of science protocols. A user may create a science protocol by inputting information relating to one or more steps of an experiment. The created science protocol may be stored in the protocol database. A user may search the protocol database using a navigable menu for accessing a plurality of application functionalities associated with the protocol database. Based on the search, a user may be able to retrieve and download the created science protocol. The user may be able to modify and/or annotate the created science protocol. The modified and/or annotated science protocol may be stored in the protocol database as a modified and/or annotated version of the created science protocol.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims priority of U.S. Provisional. Application Nos.61/776,472, filed Mar. 11, 2013, and 61/673,624, filed Jul. 19, 2012,the contents of which are hereby incorporated by reference.

TECHNICAL FIELD

This disclosure relates to tools, such as systems, apparatuses,methodologies, computer program products, etc., for providing auser-populated online repository of science protocols.

BACKGROUND

In the field of biomedical sciences, chemistry, medicine and otherrelated disciplines, protocols are used to record or document laboratoryexperiments. However, there has been no easy way of managing a pluralityof such protocols, and similarly, no convenient way of publishing orsharing such protocols.

There have been many attempts at creating a protocol repository over thepast years. However, all have failed because of the impossible task ofreaching out to laboratories and manually entering one protocol at atime.

There is a need for a more convenient way of building and maintaining aprotocol repository.

SUMMARY

This disclosure provides tools (in the form of apparatuses,methodologies and systems) for allowing users to create and edit scienceprotocols, upload such science protocols onto an online protocolrepository, and download science protocols uploaded by other users fromthe online protocol repository.

In an aspect of this disclosure, a repository apparatus provides a userregistration function to register a user, a protocol submission functionto register a specific protocol in a protocol database, and a protocolsearch function to search the protocol database based on specified keywords and search options.

In another aspect of this disclosure, an application user interfaceapparatus includes a creation part configured to provide a protocolcreation user interface, receive a series of user inputs entered by theuser through the protocol creation user interface, create a new protocolbased on the series of user inputs, and add the new protocol to a localprotocol database, a modification part configured to provide a protocolmodification user interface, receive a user selection of a specificprotocol of the plurality of protocols and a series of user inputsentered by the user through the protocol modification user interface,and modifying the specific protocol based on the series of user inputs.All output part configured to provide a protocol output user interface,receive a user selection of a specific protocol of the plurality ofprotocols and a destination specified by the user, and outputting thespecific protocol to the specified destination, and a download partconfigured to allow the user to (i) download a protocol from theprotocol database by communicating with the repository apparatus or (ii)import a protocol from a text file or e-mail.

In another aspect of this disclosure, a system provides a web-basedrepository of science protocols. The system may comprise a repositoryapparatus configured to execute a protocol management application thatincludes a plurality of application functionalities, the applicationfunctionalities including: a user registration function to register auser, a protocol submission function to register a specific protocol ina protocol database, and a protocol search function to search theprotocol database based on specified keywords and search options. Therepository apparatus may include a web interface part configured toprovide a user with navigable menu for accessing the plurality ofapplication functionalities. The system may further include anapplication user interface apparatus configured to communicate with theprotocol management application, the application user interfaceapparatus including a processor and a non-transitory storage mediumembodying instructions executable by the processor to configure theapplication user interface apparatus to include: a creation partconfigured to provide a protocol creation user interface, receive aseries of user inputs entered by a user through the protocol creationuser interface and create a new protocol based on the series of userinputs, a modification part configured to provide a protocolmodification user interface, receive a user selection of a specificprotocol of the plurality of protocols and a series of user inputsentered by a user through the protocol modification user interface, andmodify the specific protocol based on the series of user inputs; anoutput part configured to provide a protocol output user interface,receive a user selection of a specific protocol of the plurality ofprotocols and output the specific protocol to one or more destinations;and a download part configured to allow the user to (i) download aprotocol from the protocol database by communicating with the repositoryapparatus or (ii) import a protocol from a text file or e-mail to therepository apparatus.

In another aspect of this disclosure, a protocol management apparatusmay be provided including a processor and a non-transitory storagemedium embodying instructions executable by the processor to configurethe application user interface apparatus to include: a creation partconfigured to provide a protocol creation user interface, receive aseries of user inputs entered by a user through the protocol creationuser interface, create a new protocol based on the series of userinputs, and add the new protocol to a protocol database; a modificationpart configured to provide a protocol modification user interface,receive a user selection of a specific protocol of the plurality ofprotocols and a series of user inputs entered by a user through theprotocol modification user interface, and modify the specific protocolbased on the series of user inputs; an output part configured to providea protocol output user interface, receive a user selection of a specificprotocol of the plurality of protocols and output the specific protocolto the one or more destinations; and a display part configured todisplay a list of the plurality of protocols stored in the protocoldatabase.

In another aspect of this disclosure, a processor-implemented method forproviding a web-based repository of science protocols may be provided.The method may comprise providing a protocol database for containing aplurality of scientific protocols; allowing one or more users to createone or more scientific protocols; storing the one or more createdscientific protocols in the protocol database; allowing the one or moreusers to search of the protocol database by using a navigable menu foraccessing a plurality of application functionalities associated with theprotocol database; retrieving the one or more created scientificprotocols from the protocol database based on the search; and allowingthe one or more users to view or download the one or more createdscientific protocols.

The method may further comprise allowing the one or more users toannotate the one or more created scientific protocols by submitting oneor more annotations to the one or more created scientific protocols; andstoring the one or more annotations to the one or more createdscientific protocols in the protocol database.

According to one embodiment, each of the one or more annotations to theone or more created scientific protocols in the protocol database areseparately stored as additional entries associated with the one or morecreated scientific protocols.

The method may further comprise allowing one or more users to conductone or more additional searches of the protocol database by using anavigable menu for accessing a plurality of application functionalitiesassociated with the protocol database; retrieving one or more annotatedscientific protocols from the protocol database based on the one or moreadditional searches; and allowing one or more users to view or downloadthe one or more annotated scientific protocols from the protocoldatabase.

According to one embodiment, the one or more annotated scientificprotocols are displayed in addition to one or more originally createdscientific protocols.

The method may further comprise allowing a protocol managementapplication to communicate with a lab device to automatically configurethe lab device based on the one or more created scientific protocols orbased on the one or more annotated scientific protocols.

The method may further comprise allowing a protocol managementapplication to communicate with a lab device to monitor a status of thelab device based on the one or more created scientific protocols orbased on the one or more annotated scientific protocols.

BRIEF DESCRIPTION OF THE DRAWINGS

The aforementioned and other aspects, features and advantages can bebetter understood from the following detailed description with referenceto the accompanying drawings wherein:

FIG. 1 shows a block diagram of a system, according to an exemplaryembodiment;

FIG. 2A shows a sample menu screen, according to an exemplaryembodiment;

FIG. 2B shows another sample menu screen, according to an exemplaryembodiment;

FIG. 2C-2E show sample screens of protocol tracking, according to anexemplary embodiment;

FIG. 2F shows a sample screen showing annotations, according to anexemplary embodiment;

FIG. 2G shows another sample screen showing annotations, according toanother exemplary embodiment;

FIG. 2H shows a sample message displayed to the user, according toanother exemplary embodiment;

FIG. 2I shows a sample message displayed to the user, according toanother exemplary embodiment;

FIG. 3 shows a block diagram of a system, according to another exemplaryembodiment; and

FIG. 4 shows a block diagram of an exemplary configuration of a terminalfor running applications shown in FIG. 1.

FIG. 5 shows a block diagram of a system, according to another exemplaryembodiment.

FIG. 6 shows a flow-chart illustrating a processor-implemented methodfor providing a web-based repository of science protocols according toan exemplary embodiment.

DETAILED DESCRIPTION

This disclosure provides tools (in the form of apparatuses,methodologies and systems) for allowing users to access a web-basedrepository of science protocols. Such service can be provided through aweb-based server via the Internet. In other embodiments, the server neednot be a web-based server and may comprise any type of server. Likewise,in other embodiments, the service may be provided through other meansbesides via the Internet.

In describing examples and exemplary embodiments illustrated in thedrawings, specific terminology is employed for the sake of clarity.However, this disclosure is not intended to be limited to the specificterminology so selected, and it is to be understood that each specificelement includes all technical equivalents that operate in a similarmanner.

Referring now to the drawings, wherein like reference numerals designateidentical or corresponding parts throughout the several views, FIG. 1shows a block diagram of a system 100, according to an exemplaryembodiment of the present disclosure. The system 100 includes acloud-based repository of protocols 101, applications 102 and 103 and anetwork 104 through which the repository 101 and the applications 102and, 103 communicate. Those skilled in the art will appreciate that therepository needs not be cloud-based but can comprise any type ofrepository of protocols while remaining within the scope of the currentdisclosure.

As used herein, the term repository apparatus may include, but is notlimited to, a processor and a storage medium. The repository apparatus'storage medium may contain a protocol management application executableby the processor.

The cloud-based repository of protocols 101 may include free, up-to-dateand evolving protocols in biomedical sciences, chemistry, medicine, andother disciplines. A social network layer will enable scientists toconnect by expertise, with geographically proximal option, totroubleshoot the use of similar techniques. The social network layer mayenable scientists to connect based on various criteria, such asexpertise, geographic proximity, profession, research collaboration,etc.

The repository 101 may be accessible by users on a web site via a webinterface that includes a menu for allowing the users to navigate todifferent parts of the website. The web site may include the protocolrepository as well as other sections such as news, jobs and/orpublications. The website preferably includes links to a login screen,FAQ (frequently asked questions) and contacts.

The pages of the web site may have two different states: one foranonymous users and another for logged-in registered users. The web sitemay also include further states for users such as system administrators.

The protocol repository page may include an index providing quicknavigation into a particular scientific domain.

The users may also search the protocol database by keywords and/orfilter by reagents, type of protocol and/or scientific domain.

On a page for a particular protocol, the protocol is preferablydisplayed with the author's name and the dates of creation and lastrevision.

Users may vote up or vote down a particular protocol, and the repositorymay maintain a running score (i.e. rating) for each of the protocols.For example, a protocol with a high rating may be shown before anotherprotocol with a lower rating. The users may also flag a particularprotocol as spam or share the particular protocol with other users, forexample, via e-mail or other social networking web site. Access to suchfeatures may be limited to logged-in registered users.

The web site may also include a notification feature in which anotification is sent to any users who have downloaded a particularprotocol when the particular protocol is modified by the author (oranother user) of the protocol.

The web site preferably allows users to upload a protocol, eitherthrough an application (e.g. the application 102) or a web browser on aterminal device (e.g. a desktop), or by way of any other means ofuploading. When such a protocol is uploaded to the online protocolrepository (i.e. repository 101), the protocol (or protocol stepsthereof) may be associated with other protocols existing on the protocolrepository and/or publications with citation information (e.g. journal,author, date, manuscript title).

The web site may also allow the users to create protocols in a mannersimilar to that discussed infra in connection with the application 102.

The website preferably has a way of standardizing protocol submission.For example, when a protocol is uploaded or created, the steps in theprotocol may be checked and/or edited to improve consistency and/or aidin automated categorization and comparison of submissions (e.g. if astep is described as “spin” or “centrifugation”, all such terms will bechanged to “spin”). Alternatively or additionally, the web site may alsoimplement and/or enforce certain guidelines upon user submission ofprotocols and/or reject non-complying protocols rather than acceptingthe protocols and automatically editing the accepted protocols.

The web site may also include a feature for automatically flaggingprotocol discrepancies and/or identifying variable steps in eachprotocol, based on comparison of submitted instances (i.e. steps). Thisfeature may allow scientists to trouble-shoot, optimize, and/or sampledifferent parameters when adopting any protocol to their particular laband/or use.

The web site may also have a feature for displaying new publishedmanuscript suggestions based on the one or more type of protocols and/orother publications that a particular registered user may have searched.Similarly, based on the registered user's history of searches, refinedand ranked search results of scientific literature may be displayed tothe registered user.

Returning to the system 100 of FIG. 1, the application 102 may allow anapplication user to perform a variety of tasks related to protocolmanagement. For example, the application 102 may allow the applicationuser to create a new protocol entry. The application user may be askedto input each step of an experiment using a user interface (e.g. textfields including sequential step number, step name, duration, reagent,amount, description and warning/reminder). The sequential step number ispreferably automatically entered and/or automatically incremented. Alluser-entered fields are optional, and each protocol preferably has aunique name.

The application user may also import a protocol from a source, forexample, a CSV (comma separated values) file). In addition, theapplication user may also use an e-mail containing a properly formattedtext (either in the body of the e-mail or as an e-mail attachment) toimport a protocol. In some embodiments, the imported protocol is storedin a personal protocol database, which may be implemented using a localmemory device and/or via a network (e.g. cloud storage of theapplication user). In other embodiments, the imported protocol may bestored in any other type of storage medium.

Additionally, the application user may download a protocol from aweb-based protocol repository (e.g. the cloud-based repository ofprotocols 101 of FIG. 1). In order to download a protocol from theweb-based protocol repository, the application user is preferablyrequired to enter login credentials recognized by the protocolrepository management system managing the repository.

The protocols that are created, imported and/or downloaded arepreferably organized under folders and/or headings that areuser-specified and/or automatically generated based on the nature of theprotocols. For example, headings such as “RNA Protocols”, “DNAProtocols” and “Protein Protocols” may be used, as shown in FIG. 2B. Theuser-created protocols may also be organized separately from theimported/downloaded protocols.

In some embodiments, the user can also specify and cause the application102 to maintain at least one separate section for favorite and/orfrequently-used protocols (or reagents discussed below).

The application user may also modify and/or annotate the protocolsstored in the personal, protocol database or other type of protocoldatabase. For example, a prolonged touch of a given step (i.e. row) mayopen a text edit field for allowing the user to provide modificationsand/or annotations to the existing, stored protocol.

In some embodiments, the user may submit one or more annotations to anexisting stored protocol. In this embodiment, the user would submit theannotated information as an additional layer to the existing protocol.Thus, the one or more annotations can be saved as additional layers tothe existing, stored protocol, with the ability to export a record ofthe entire experiment (i.e. annotated protocol), step-by-step. Forexample, if a user provides an annotation for several steps of theexisting stored protocol, each of those annotations can be storedseparately for each step of the experiment. In some embodiments, thechanges and/or annotations may be indented and displayed underneath therespective step in the originally created protocols. In suchembodiments, the annotated protocols may be stored in the protocoldatabase as annotated versions of the originally created protocols.Thus, when a user later obtains or downloads an annotated protocol, forexample, from the protocol database, the user will see the originallycreated protocol along with the tracked annotations made thereto. Thoseannotations can be designated in such a way so that it is readilyapparent that they are additions made by one or more users. According toone embodiment, the one or more annotations may be displayed in any formsufficient to indicate that they are annotations and/or modifications tothe originally created protocol, for example, in the form ofunderlining, indenting, designations as “annotations” in a separatesection in connection with each respective step, or any other type ofdisplay sufficient to indicate that the information is annotatedinformation.

It should be readily apparent to one of ordinary skill in the art thatthere are one or more users using the system of the present invention.If several users make one or more annotations to any given protocol,each of the annotations made by each user can be separately stored inthe protocol database and can be indented and displayed underneath eachrespective step in the originally created one or more protocols.

According to an embodiment, the author and/or entry date of each of theone or more annotations may also be visible to the user. Suchinformation may assist the user in deciding when to follow a step aswritten by the original author and when to follow a step as written by asubsequent author. As a result, the disclosed application provides auser with the ability to instantly see all modified and optimizedchanges for a given step of a given protocol.

In some embodiments, user-submitted modifications and/or annotations tothe protocols may be stored as separate, modified protocol entries inthe protocol database. Thus, when a user saves the one or more modifiedprotocols, the user is submitting separate modified protocols, with therepository now storing two or more versions, both the original protocoland the modified protocols. In turn, when one or more users latersearches for the protocol, the protocol database may retrieve at leasttwo search results: the original protocol and at least one modifiedprotocol. As a result, for a given protocol, the disclosed applicationprovides users with various options of the protocol to follow. Forexample, users may decide to download a particular modified protocolbecause it is the most current or has received the highest user ratingcompared to other modified protocols generated by the search.Alternatively, users may instead decide to download the original versionof the protocol because it was written by a notable professor.

In some embodiments, user-submitted modifications and/or annotations tothe published protocols may operate to overwrite the existing protocol.In such cases, the protocol database may store the modified protocol byreplacing an existing protocol with an updated protocol that includesthe modifications and/or annotations. In turn, when an application userlater searches for the protocol after it has been modified and/orannotated, the most current and up-to-date modified protocol will beprovided to the application user.

Additionally, data relating to reagents (e.g. substance or compound usedin the protocols) can also be created, imported and downloaded in asimilar manner. The reagents are preferably tagged as “reagents” and maybe stored and displayed separately from the protocols. The reagents canalso be directly (or indirectly) linked to the “reagent field” of anyprotocol. For example, when creating a new protocol, to populate thereagent field of the protocol, the user may be able to select from alist of reagents currently stored in the personal reagent database, forexample, using a drop-down option.

When going through an experiment, a prolonged touch of a reagentdisplayed, for example, on a mobile screen should bring up the reagent'srecipe, if such recipe has been entered.

Also, the application user can select a protocol to run (i.e. to conductthe experiment). When the user selects the protocol to run, the protocolinstance becomes a record of the particular execution on that day, thusacting as a digital lab notebook. In addition, the application 102 maydisplay a checklist of all the steps included in the protocol, and theapplication user may be able to check off each step as he or shecompletes the step. For example, as shown in FIGS. 2C-2E, the user maybe able to check off the checkboxes associated with the steps as he orshe completes each step. For example, the application 102 may alert theuser when it is time to move onto the next step (e.g. 30 minutes afterstep 1 is started).

The application 102 may also interface with laboratory equipment forautomatic notifications and/or error checking. For instance, if acentrifugation step requires a 10-minute spin according to the protocolin the application 102, and the user attempts to activate the centrifugefor 30 minutes, the application 102 will display a warning (e.g.,indicating that the user attempt deviates from the protocol, such asshown in FIG. 2H). In some embodiments, an application may be configured(e.g., via a user configuring a Settings feature) to display a warningfor some but not all deviations between a user's equipment input and anapplication's protocol. For example, the application may be configuredto warn the user, only if the protocol and/or step of the protocol wascreated and/or modified by an author with a predetermined level oftrustworthiness (e.g., by a Professor at a University, by a scientistwho is part of a well-respected research collaboration, etc.). Dataindicative of authors' trustworthiness may be stored in the repository.In some embodiments, data indicative of authors' trustworthiness issafeguarded (e.g., by a system administrator and/or by entry of theauthor's credentials) in order to preserve the integrity of suchinformation in the repository. In some embodiments, the application maybe configured to warn the user if the protocol and/or step of theprotocol was authored and/or modified by another entity participating inthe user's research collaboration, to thereby help ensure continuitythroughout the collaboration. In some embodiments, the application maybe configured to warn the user only if the protocol received a userscore (e.g., a user rating) above a predetermined threshold. In someembodiments, the application may be configured to warn the user only ifthe user's equipment input differs from the protocol by a predeterminedamount (e.g., only if the time in the centrifuge differs by more than 5minutes). In some embodiments, lab devices may be configured tocommunicate with the application. For example, lab equipment may beconfigured to send a notification to the application indicating that astatus of the lab equipment has changed. For example, the centrifuge maycommunicate to the application 102 when the spin is finished, with thealert transmitted to the user (e.g., notifying the user that he or sheis ready to move onto the next step, such as shown in FIG. 21). Further,if the protocol specifies the settings (e.g. speed, temperature, time,etc.) for the laboratory equipment to be used for a particular step, theapplication 102 may communicate with the laboratory equipment to causesuch settings to be automatically loaded onto the laboratory equipment.Thus, in an exemplary embodiment, when the application user initiates acentrifugation step requiring a 10-minute spin, the application 102automatically configures the centrifuge to be activated for 10 minutes.In some embodiments, an application may be configured (e.g., via a userSettings feature) to automatically configure laboratory equipment forsome but not all instances. For example, in some embodiments, theapplication may be configured to automatically configure laboratoryequipment only if the protocol and/or step of the protocol was createdand/or modified by an author with a predetermined level oftrustworthiness. In some embodiments, the application may be configuredto automatically configure laboratory equipment if the protocol and/orstep of the protocol was authored and/or modified by another entityparticipating in the user's research collaboration, to thereby helpensure continuity throughout the collaboration. In some embodiments, theapplication may be configured to automatically configure laboratoryequipment only if the protocol has received a user score (e.g., a userrating) above a predetermined threshold. In some embodiments, theapplication may be configured to automatically configure certainpre-selected laboratory equipment and not other pre selectedautomatically configure laboratory equipment.

For example, FIG. 5 shows a block diagram of a system, according to anexemplary embodiment. As shown in FIG. 5, an application 501 a isrunning on a terminal 501, and the terminal 501 communicates with labdevices 502-504 via a network 509.

The operation of the application 501 a is similar to that of theapplication 102 described supra with reference to FIG. 1.

The network 509 can be a local area network, a wide area network or anytype of network such as an intranet, an extranet (for example, toprovide controlled access to external users, for example through theInternet), the Internet, etc., or a combination thereof. Further, othercommunication links (such as a virtual private network, a wireless link,etc.) may be used as well for the network 509. In addition, the network509 preferably uses TCP/IP (Transmission Control Protocol/InternetProtocol), but other protocols such as SNMP (Simple Network ManagementProtocol) and HTTP (Hypertext Transfer Protocol) can also be used. Howdevices can connect to and communicate over networks is well-known inthe art and is discussed for example, in “How Networks Work”, by FrankJ. Derfler, Jr. and Les Freed (Que Corporation 2000) and “How ComputersWork”, by Ron White (Que Corporation 1999), the entire contents of eachof which are incorporated herein by reference.

It should be appreciated that although one terminal and three labdevices are shown in FIG. 5, the system 500 is not limited to suchconfiguration and may include any arbitrary number of terminals and labdevices.

In addition, each step of a protocol may also be expanded to display adetailed view of the step. Any changes and/or annotations previouslymade to a particular step may be displayed along with the particularstep, as shown in FIG. 2F. In another exemplary embodiment, theannotator may have a view as illustrated in FIG. 2G. The applicationuser may be allowed to change and/or annotate the steps directly on theapplication. Several protocol instances can be tracked in the abovemanner concurrently (that is, two or more protocols may be tracked inparallel in the application).

When the application user first opens the application 102, the user maysee a menu screen for navigating through different functionalities ofthe application. For example, as shown in FIG. 2A, the menu screen mayinclude a plurality of buttons for allowing the user to access thevarious functionalities of the application.

In addition, in some embodiments, the application user may also exportand/or upload the protocols and/or reagents stored in the personaldatabase or in another type of database. Such protocols and/or reagentscan be exported and/or uploaded through any means such as by e-mailingthe protocols and/or reagents to another user, transferring theprotocols and/or reagents to another application user, and/or uploadingthe protocols and/or reagents to the web-based protocol repository.

As shown in FIG. 1, the applications 102 and 103 may also communicate toexchange protocols and/or reagents, for example, using the import/exportfeature of the application.

Although only two applications are shown in FIG. 1, it should beunderstood that the system 100 can include a plurality of otherapplications (which can have similar or different configurations fromone another).

Further, the applications 102 and 103 can be, for example, desktopapplications that can be used by desktop users and/or mobileapplications that can be used by mobile device users. Although not shownin FIG. 1, each of the applications 102 and 103 (or similarapplications) is executed on a terminal device, including but notlimited to a personal, notebook or workstation computer, a kiosk, a PDA(personal digital assistant), a mobile phone or handset, anotherinformation terminal, etc., that can communicate with other devicesthrough the network 104, which can be, for example, the Internet.

By way of the aforementioned features of the repository 101 and theapplications 102 and 103, the system 100 of FIG. 1 provides scientistsand lab workers with the ability to structure the protocols for theirexperiments, reduce errors through interfacing with laboratoryequipment, keep the protocols up to date, discover new protocols,connect with scientists working on similar projects and/or facilitatescientific collaboration. For example, as discussed above, scientistsmay use the application to track their progress throughout experimentsin a form of protocols that are lists of steps with instructions.Scientists can also enter annotations, save protocols to the localdevice (thus using the application as a digital lab notebook), and/orshare with other scientists without uploading to the centralizedrepository Or submit the protocols to the centralized repository.Submitting a protocol to the centralized repository may be viewed asessentially publishing the protocol for the community. Once published,other scientists will be able to download protocols to their own devicesand use them. Scientists can change an existing protocol if theydiscover imperfections in the original. The applications 102 and 103 maycommunicate with the cloud based centralized repository 101 and betweeneach other via a set of proprietary APIs (e.g. ZappyLabAPI), forexample, located on an API server 303 shown in FIG. 3. The repositoryhas a web-based interface for allowing users to view submittedprotocols, search by keyword or protocol features as well as discoverand communicate with other scientists.

Preferably, no user login or any other credentials are required to usethe mobile application. However, in order to submit or access protocolsin the repository users may be required to register by providing basicpersonal information such as their name, location and field of research.

An example of a configuration of a terminal on which the applications102 and 103 of FIG. 1 may run is shown schematically in FIG. 4. In FIG.4, computer 400 includes a controller (or central processing unit) 402that communicates with a number of other components, including memory403, display 404, keyboard (and/or keypad) 406, other input/output (suchas mouse, touchpad, stylus, microphone and/or speaker with voice/speechinterface and/or recognition software, etc.) 407, network interface 408and application software 405, by way of an internal bus 401.

The memory 403 can provide storage for program and data, and may includea combination of assorted conventional storage devices such as buffers,registers and memories [for example, read-only memory (ROM),programmable ROM (PROM), erasable PROM (EPROM), electrically erasablePROM (EEPROM), static random access memory (SRAM), dynamic random accessmemory (DRAM), non-volatile random access memory (NOVRAM), etc.].

The network interface 408 provides a connection (for example, by way ofan Ethernet connection or other network connection which supports anydesired network protocol such as, but not limited to TCP/IP, IPX,IPX/SPX, or NetBEUI) to network 401.

Application software 405 is shown as a component connected to theinternal bus 401, but in practice is typically stored in storage mediasuch as a hard disk or portable media, and/or received through thenetwork 401, and loaded into memory 403 as the need arises.

Depending on the type of the particular terminal device, one or more ofthe components shown in FIG. 4 may be missing. For example, a particularmobile phone may be missing the keyboard 406.

Additional aspects or components of the computer 400 are conventional(unless otherwise discussed herein), and in the interest of clarity andbrevity are not discussed in detail herein. Such aspects and componentsare discussed, for example, in “How Computers Work”, by Ron White (QuoCorporation 1999), and “How Networks Work”, by Frank J. Derfler, Jr. andLes Freed (Que Corporation 2000), the entire contents of each of whichare incorporated herein by reference.

FIG. 6 shows a flow-chart illustrating a processor-implemented methodfor providing a web-based repository of science protocols according toone embodiment. Step 601 comprises providing a protocol database forcontaining a plurality of scientific protocols. The protocol databasemay be web-based. Step 602 comprises allowing one or more users tocreate one or more scientific protocols. Creating one or more scientificprotocols may comprise using a user interface to input informationrelating to one or more steps of an experiment, including step number,step name, duration, reagent, amount, description, a warning, and/or areminder. Step 603 comprises storing the one or more created scientificprotocols in the protocol database. Step 604 comprises allowing the oneor more users to conduct a search of the protocol database by using anavigable menu for accessing a plurality of application functionalitiesassociated with the protocol database. According to an embodiment,conducting a search may be based on specified keywords and/or searchoptions such as reagents, a type of protocol, and/or a scientificdomain. Step 605 comprises retrieving the one or more created scientificprotocols from the protocol database based on the search. The retrievalof the one or more created scientific protocols may be recorded as aprotocol instance, thus serving as a digital lab notebook. Step 606comprises allowing the one or more users to view or to download the oneor more created scientific protocols.

Step 607 comprises allowing one or more users to annotate the one ormore created scientific protocols by submitting one or more annotationsto the one or more created scientific protocols. Step 608 comprisesstoring the one or more annotations to the one or more createdscientific protocols in the protocol database. According to anembodiment, each of the one or more annotations to the one or morecreated scientific protocols may be stored separately as additionalentries associated with the one or more scientific protocols. In thisway, the one or more annotated scientific protocols may be displayed tothe one or more users in such a way as to show every single annotationmade to a given scientific protocol by the one or more users along withoriginally created scientific protocol. Step 609 comprises allowing theone or more users to conduct one or more additional searches of theprotocol database by using a navigable menu for accessing a plurality ofapplication functionalities associated with the protocol database. Step610 comprises retrieving one or more annotated scientific protocols fromthe protocol database based on the one or more additional searches. Step611 comprises allowing one or more users to view or download the one ormore annotated scientific protocols from the protocol database.According to an embodiment, the one or more users are able to see andtrack annotations previously made to the original one or more createdscientific protocols.

According to another embodiment, the one or more users may be able tomodify and/or annotate the one or more created scientific protocols tocreate one or more modified scientific protocols. Such embodiment maycomprise storing separately in the protocol database both the originalone or more created scientific protocols and the one or more modifiedscientific protocols. Such embodiment may further comprise allowing oneor more users to conduct one or more additional searches of the protocoldatabase, and retrieving the one or more modified scientific protocolsand/or the original one or more scientific protocols from the protocoldatabase. The embodiment may further comprise allowing one or more usersto view or download the one or more modified scientific protocols and/orthe original one or more created scientific protocols. According to thisembodiment, the one or more users may have the option to view either theoriginal created scientific protocol or any one of the modified versionsof the scientific protocol.

According to another embodiment, the one or more users may be able tomodify and/or annotate the one or more created scientific protocols tooverwrite the original one or more created scientific protocols tocreate one or more modified scientific protocols. Such embodiment maycomprise storing in the protocol database the one or more modifiedscientific protocols by replacing the original one or more createdscientific protocols with the one or more modified scientific protocols.Such embodiment may further comprise allowing one or more users toconduct one or more additional searches of the protocol database, andretrieve the one or more modified scientific protocols from the protocoldatabase. Such embodiment may further comprise allowing one or moreusers to view or to download the one or more modified scientificprotocols.

According to an embodiment, a protocol management application may beallowed to communicate with a lab device (e.g., to monitor a status ofthe lab device, to monitor a setting of the lab device, and/or toautomatically configure a setting of the lab device) based on the one ormore created scientific protocol and/or based on the one or moremodified scientific protocol. The method may include allowing a protocolmanagement application to communicate with a lab device to automaticallyconfigure the lab device based on the one or more created scientificprotocols and/or annotated scientific protocols and/or modifiedscientific protocols. In some embodiments, the method may includeallowing a protocol management application to communicate with a labdevice to monitor a status of the lab device based on the one or morecreated scientific protocols and/or annotated scientific protocolsand/or modified scientific protocols. Some of the advantages of thepresent disclosure, which are not limited to those provided hereinafter,include:

(1) revolutionized scientific laboratory practice and more efficientresearch due to ready availability of a user-populated protocolrepository

(2) a new venue for researchers to share new method findings

(3) a new structure to assign credit to scientists who improve andmodify existing protocols;

(4) minimization of experimental procedure errors through communicationbetween the user's mobile or desktop device and laboratory equipment.

The above-mentioned embodiments and examples are illustrative, and manyvariations can be introduced on these embodiments without departing fromthe spirit of the disclosure or from the scope of the appended claims.For example, elements and/or features of different illustrativeembodiments may be combined with each other and/or substituted for eachother within the scope of this disclosure and appended claims.

What is claimed:
 1. A system for providing a web-based repository ofscience protocols, the system comprising: a repository apparatusconfigured to execute a protocol management application that includes aplurality of application functionalities, the applicationfunctionalities including a user registration function to register auser, a protocol submission function to register a specific protocol ina protocol database, and a protocol search function to search theprotocol database based on specified keywords and search options, therepository apparatus including a web interface part configured toprovide a user with a navigable menu for accessing the plurality ofapplication functionalities; and an application user interface apparatusconfigured to communicate with the protocol management application, theapplication user interface apparatus including a processor and anon-transitory storage medium embodying instructions executable by theprocessor to configure the application user interface apparatus toinclude: a creation part configured to provide a protocol creation userinterface, receive a series of user inputs entered by the user throughthe protocol creation user interface, create a new protocol based on theseries of user inputs, and add the new protocol to a local protocoldatabase; a modification part configured to provide a protocolmodification user interface, receive a user selection of a specificprotocol of the plurality of protocols and a series of user inputsentered by the user through the protocol modification user interface,and modifying the specific protocol based on the series of user inputs;an output part configured to provide a protocol output user interface,receive a user selection of a specific protocol of the plurality ofprotocols and a destination specified by the user, and outputting thespecific protocol to the specified destination; and a download partconfigured to allow the user to (i) download a protocol from theprotocol database by communicating with the repository apparatus or (ii)import a protocol from a text file or e-mail.
 2. The system of claim 1,wherein the search options selectable by the user include at least oneof reagents, a type of protocol and a scientific domain.
 3. The systemof claim 1, wherein the application functionalities further include: avote function to either increase a score of a specified protocol in acase that the user votes up the specified protocol or decrease the scoreof the specified protocol in a case that the user votes down thespecified protocol; a share function to output the specified protocol toan output destination specified by the user; a spam-flag function toincrease a spam score of the specified protocol in a case that the usermarks the specified protocol as spam, and to hide the specified protocolin a case that the spam score exceeds a predetermined value; and anotification function to output a notification to each user who hasdownloaded the specified protocol, when the specified protocol ismodified by an author or another user of the specified protocol.
 4. Aprotocol management apparatus including a processor and a non-transitorystorage medium embodying instructions executable by the processor toconfigure the protocol management apparatus to include: a creation partconfigured to provide a protocol creation user interface, receive aseries of user inputs entered by the user through the protocol creationuser interface, create a new protocol based on the series of userinputs, and add the new protocol to a local protocol database; amodification part configured to provide a protocol modification userinterface, receive a user selection of a specific protocol of theplurality of protocols and a series of user inputs entered by the userthrough the protocol modification user interface, and modifying thespecific protocol based on the series of user inputs; an output partconfigured to provide a protocol output user interface, receive a userselection of a specific protocol of the plurality of protocols and adestination specified by the user, and outputting the specific protocolto the specified destination; and a display part configured to displayto the user a list of the plurality of protocols stored in the localprotocol database.
 5. The apparatus of claim 4, wherein the protocolcreation user interface allows the user to create a new protocol byinputting one step at a time, each step including at least one of asequential step number, a step name, a duration, a reagent, an amount, adescription, a warning or reminder.
 6. The apparatus of claim 4, whereinthe text file is a comma-separated values (CSV) file.
 7. The apparatusof claim 4, wherein the display part displays a navigable menu includinga plurality of menu items, each menu item including either a list of oneor more protocols stored in the local protocol database or anothernavigable menu.
 8. The apparatus of claim 4, wherein the protocolmodification user interface provides the user with a text field forreceiving an annotation for a specified step of the specified protocol.9. The apparatus of claim 4, wherein when the display part receives auser selection of a specific protocol, the display part displays theprotocol to the user, including each step of the protocol andannotations corresponding to said each step.
 10. The apparatus of claim4, further comprising a lab device interface part configured tocommunicate step-specific settings to a lab device to automaticallyconfigure the lab device based on the step-specific settings.
 11. Theapparatus of claim 4, further comprising a lab device interface partconfigured to communicate with a lab device to ensure operations of thelab device complies with a particular step in a protocol, wherein, in acase that the operations of the lab device deviates from said particularstep, the lab device interface part causes a warning message to bedisplayed on the protocol management apparatus, indicating that heoperations of the lab device has deviated from said particular step. 12.The apparatus of claim 4, further comprising a lab device interface partconfigured to communicate with a lab device to monitor a status of thelab device, wherein, when the status of the lab device is changed, thelab device interface part causes a message to be displayed on theprotocol management apparatus, indicating that the status of the labdevice has been changed.